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Yorodumi- EMDB-9032: Full-length S. pombe Mdn1 in the presence of AMPPNP (ring region) -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-9032 | |||||||||
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Title | Full-length S. pombe Mdn1 in the presence of AMPPNP (ring region) | |||||||||
Map data | Full-length S. pombe Mdn1 in the presence of AMPPNP (ring region), primary map | |||||||||
Sample |
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Function / homology | Function and homology information preribosome, large subunit precursor / ribosomal large subunit export from nucleus / ribosomal large subunit biogenesis / ribosome biogenesis / calcium ion binding / nucleolus / ATP hydrolysis activity / nucleoplasm / ATP binding / nucleus Similarity search - Function | |||||||||
Biological species | Schizosaccharomyces pombe (fission yeast) / Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.0 Å | |||||||||
Authors | Chen Z / Suzuki H / Wang AC / DiMaio F / Walz T / Kapoor TM | |||||||||
Citation | Journal: Cell / Year: 2018 Title: Structural Insights into Mdn1, an Essential AAA Protein Required for Ribosome Biogenesis. Authors: Zhen Chen / Hiroshi Suzuki / Yuki Kobayashi / Ashley C Wang / Frank DiMaio / Shigehiro A Kawashima / Thomas Walz / Tarun M Kapoor / Abstract: Mdn1 is an essential AAA (ATPase associated with various activities) protein that removes assembly factors from distinct precursors of the ribosomal 60S subunit. However, Mdn1's large size (∼5,000 ...Mdn1 is an essential AAA (ATPase associated with various activities) protein that removes assembly factors from distinct precursors of the ribosomal 60S subunit. However, Mdn1's large size (∼5,000 amino acid [aa]) and its limited homology to other well-studied proteins have restricted our understanding of its remodeling function. Here, we present structures for S. pombe Mdn1 in the presence of AMPPNP at up to ∼4 Å or ATP plus Rbin-1, a chemical inhibitor, at ∼8 Å resolution. These data reveal that Mdn1's MIDAS domain is tethered to its ring-shaped AAA domain through an ∼20 nm long structured linker and a flexible ∼500 aa Asp/Glu-rich motif. We find that the MIDAS domain, which also binds other ribosome-assembly factors, docks onto the AAA ring in a nucleotide state-specific manner. Together, our findings reveal how conformational changes in the AAA ring can be directly transmitted to the MIDAS domain and thereby drive the targeted release of assembly factors from ribosomal 60S-subunit precursors. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_9032.map.gz | 91.8 MB | EMDB map data format | |
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Header (meta data) | emd-9032-v30.xml emd-9032.xml | 17 KB 17 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_9032_fsc.xml | 8.7 KB | Display | FSC data file |
Images | emd_9032.png | 45.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-9032 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9032 | HTTPS FTP |
-Validation report
Summary document | emd_9032_validation.pdf.gz | 489.7 KB | Display | EMDB validaton report |
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Full document | emd_9032_full_validation.pdf.gz | 489.3 KB | Display | |
Data in XML | emd_9032_validation.xml.gz | 11.3 KB | Display | |
Data in CIF | emd_9032_validation.cif.gz | 14.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9032 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9032 | HTTPS FTP |
-Related structure data
Related structure data | 6or5MC 9033C 9034C 9035C 9036C 6or6C 6orbC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_9032.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Full-length S. pombe Mdn1 in the presence of AMPPNP (ring region), primary map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.3 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : N-terminal density map of the full-length Mdn1 in the presence of...
Entire | Name: N-terminal density map of the full-length Mdn1 in the presence of AMPPNP |
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Components |
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-Supramolecule #1: N-terminal density map of the full-length Mdn1 in the presence of...
Supramolecule | Name: N-terminal density map of the full-length Mdn1 in the presence of AMPPNP type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Schizosaccharomyces pombe (fission yeast) |
Molecular weight | Theoretical: 540 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
-Macromolecule #1: Midasin
Macromolecule | Name: Midasin / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast) Strain: 972 / ATCC 24843 |
Molecular weight | Theoretical: 262.860312 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: MDVLIEWVAI YPQIYDILEH INYVPSNTLQ RLRLHQPWSK IDYDVWFLYA SDEIRETCKV KYYGETKTYG EVFVLENERI SQLHRLFVS WTVSERAEHL KNLLFDAGLS NLPLVELGGN VFFNSHVPLP CSLVLTKSTQ ENLNRITPYL VQKRPILLAG P EGIGKKFL ...String: MDVLIEWVAI YPQIYDILEH INYVPSNTLQ RLRLHQPWSK IDYDVWFLYA SDEIRETCKV KYYGETKTYG EVFVLENERI SQLHRLFVS WTVSERAEHL KNLLFDAGLS NLPLVELGGN VFFNSHVPLP CSLVLTKSTQ ENLNRITPYL VQKRPILLAG P EGIGKKFL ITQIAAKLGQ QIIRIHLSDS TDPKMLIGTY TSPKPGEFEW QPGVLTQAVI TGKWILFTNI EHAPSEVLSV LL PLLEKRQ LVIPSRGETI YAKGSFQMFA TSSMKTKILG QRLWQILDLT YQPDECVEVV STLYPVLSII CPTLYSVYKD IFD LFSQRS FLATSKIYRR LCLRDFYKFI KRVAFLYHKF MIPSDHVVIS QELQDAVFKE AIDMFGAFIP SRDGFDLVVR NVAI ELNIP PEKALQLRYS IPVFQNLEHN INIGRCSLKK LSTIRSCSTN SYAFTSSSLG LLEQLAAGVQ TNEPLLLVGE TGTGK TTTI QLLAGLLGQK VTVINMSQQT ESSDMLGGYK PINASTLGLP LHERFIDIFE QTFSSKKNAK FISMASTSAR RFRWKT CLK IWKEACKLSK TVLDGQQPLP NPQKRQKRLS NQVELRNQWA KFEKEVEDFE KVLTGGSNGF MFSFVEGALV KAVRSGH WV LLDEINLASL ETLEPIGQLL SSYESGILLS ERGDITPITP HKNFRLFGCM NPSTDVGKRE LEPSFRSRFT EIYVHSPD Q NLDDLLSIIQ KYIGSLCIGN EHVIREVAEL YQVAKSLSLD GSLVDGAGQR PHYTVRTLSR TLSYVTEIAP IYGLRRSLY EGFCMSFLTL LDHTSESLLY NHVVRFTLGE LNRDQQNAIL KQIPKVPDHS SYIAFCHYWL RRGSFPVEEQ EHYIITPFVQ KNLLNIARA CSTRMFPILI QGPTSSGKTS MIEYVAKKTG HKFVRINNHE HTDLQEYIGT YVTDDNGSLS FREGVLVEAL R NGYWIVLD ELNLAPTDVL EALNRLLDDN RELFIPETQV LVKPHPEFML FATQNPPGVY AGRKHLSRAF RNRFLEIHFD DI PENELET ILHKRCKIAP SYAAKIVQVF RELSLRRQTT RIFEQKNSFA TLRDLFRWAF REAVGYQQLA ENGYMLLAER ARD QKDKLA VQEVIEKVMK VKIDTDGIYN LDSMEIFQDM SLKEGPLSKV VWTRPMIRLF CLVWRCLLAK EPVLLVGDTG CGKT TVCQI LAECLHKELH IINAHQDTEN GDIIGAQRPV RNRSAVNYSL HSQLCEKFNV QESLDSIDDL IEKFEKLSSS EKNDN LSNL IERQIIKYRS LFEWHDGALV TAMKQGDFFL LDEISLADDS VLERLNSVLE LSRTLTLVEH SNAAVSLTAK DGFAFF ATM NPGGDYGKKE LSPALRNRFT EIWVPPMVDT EDILKIVEGK LHNNKIELAR PLVEYAKWHA NEYLYTDVIS IRDVLSA VE FINACEILDL NLVLFNAVSM VFIDALGSFT TFSLSNNLAS LHAERQRCFA KLNELAGSNI MASKSADISI KFSDSSFF I GDFGIPLGDS VESDSTYSLH TDTTLMNASK VLRALQVLKP ILLEGSPGVG KTSLITALAR ETGHQLVRIN LSDQTDLMD LFGSDVPVEG GEGGQFAWRD APFLAAMRNG HWVLLDELNL ASQSVLEGLN ACLDHRNEAY IPELDKVFKA HPNFRVFAAQ NPQHQGGGR KGLPRSFINR FSVVYVEALK EKDMIEIAAC NYHQVNEDWR LKIIKFMFRL QDNIEKDISF GSFGSPWEFN L RDTLRWLQ LLNDAPKYTC VSPADYLEVM VLHRMRTVED RVRTCELFKE VFDIDYEPRT IGFSLSSQCF KVGHSLLVRD VE RQKTLLD SQNILQSQLP VLESVITCIN KKWPCILVGD TATGKTCILR LLAAIAGAKI KEMAVNSDTD TMDLIGEYEQ IDI SRKASE LFTDLSQQLL NIVIKYRNFD NIFRETSLYT LTTTSFKTHS QAFTLLQKVV DQLDQLKIHE TLVHSLGDIH EKAR KLLAE FSASPAGRFE WFDGYLLKAV EEGHWFVLDN ANLCSPAVLD RLNSLLEHKG VLIVNEKTTE DGHPKTIKPH PNFRL FLTV NPVYGELSRA MRNRGVEIFL LKEALTEIDK KQMSLLEPAP ISSAVDTLAS NISYIKYVFE TMG(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) |
-Macromolecule #2: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
Macromolecule | Name: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / type: ligand / ID: 2 / Number of copies: 5 / Formula: ANP |
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Molecular weight | Theoretical: 506.196 Da |
Chemical component information | ChemComp-ANP: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.15 mg/mL |
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Buffer | pH: 7.5 |
Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Frames/image: 1-50 / Number real images: 8446 / Average exposure time: 15.0 sec. / Average electron dose: 88.8 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.4 µm / Nominal magnification: 22500 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL |
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Output model | PDB-6or5: |